He wrote on the Aymara language. His earliest publications appeared under the title Arte breve de la lengua aymara para introducir el Arte grande de la misma lengua (Rome, 1603), also Arte y gramatica muy copiosa de la lengua aymara etc.

The printing press having been introduced and established by the Jesuits at the Indian mission of Juli [es] in southwestern Peru, Bertonio had the following works printed there, including four in the year 1612 alone:

The publications by Bertonio are rare. Julius Platzmann published in facsimile the Arte y grammatica of 1603 and the Vocabularies. The Peruvian historian Clemente Markham claimed that Bertonio invented the name "Aymara"; the Bolivian geographer Manuel Vicente Ballivian rejected this in a pamphlet.